That actually happens a lot. Mass Effect Legendary Edition is missing a DLC because the source code was lost. Many of Square Enix's hit games like the PS1 Final Fantasy games and the PS2 Kingdom Hearts have lost the original source code and the modern ports are either based on PC ports or are rebuilt from the shipped assets.

Also I have a very strong impression Legend of Mana for PC is... emulated.

It has the same slowndowns it used to have on PSX, but somehow, worse, the game runs quite poorly during combat, stuttering when there is any new sprite on the screen.

I think they lost the source code, and made an emulator just f or this game, to allow them to shove the new "remastered" assets in (the remastered assets are just AI-processed backgrounds... quite poorly sometimes even, for example in one screen something that is clearly some grass near a fountain on PS1 became a green smudge on PC).

Neither of those examples have anything to do with if a publisher was given access to the source. Those seem to be more about those games being developed in a time when source control and backups were handled more loosely within the industry as a whole.

And that does not only apply to games, certain parts of MS office do not have source available anymore so MS has done binary patches to fix bugs, pixar almost lost part of a movie but an employee happened to have a offsite copy at their home.

EA released a remastered C&C some time ago. One of the developers involved in that described the problems they had with the video quality, the originals where lost, the best they could do was extract videos from the PlayStation port and try different AI up scaling algorithms. The result isn't pretty.

The best they could do is recreate and rerender the videos, but that's probably too costly for EA's typical remaster project.

A lot of the videos in C&C were live action

Which would almost certainly have required different actors, given the 25 years since the original release, and I imagine that would have cause a huge uproar in addition to being fairly expensive.

That was probably well out of scope of what they originally planned for as C&C had quite a lot of pre and post mission videos.

Out of scope, sure, but I agree that that option prevents "extract old video from the production version and try to upscale it automatically" from qualifying as "the best they could do".

"Best they could do" on the budget from EA.

Sure, that's fair.

Depending on the contract, publishers might have the ability to get a copy of the source code, but they certainly are not going to be monkeying around with it.

Doing a full build from scratch of a game is a complicated thing. The build systems at a game studios are quite extensive.

Even if you were given access to the version control repositories for a game I think it would probably take you quite a long time to be able to successfully export and build everything from scratch.